Starting phenix.real_space_refine (version: dev) on Tue Feb 21 07:41:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukj_26582/02_2023/7ukj_26582.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14196 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4717 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} Conformer: "B" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} bond proxies already assigned to first conformer: 4777 Chain: "B" Number of atoms: 4724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} Conformer: "B" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} bond proxies already assigned to first conformer: 4738 Chain: "C" Number of atoms: 4755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4738 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLY A 235 " occ=0.43 ... (6 atoms not shown) pdb=" O BGLY A 235 " occ=0.57 residue: pdb=" N ASER B 234 " occ=0.68 ... (10 atoms not shown) pdb=" OG BSER B 234 " occ=0.32 residue: pdb=" N AGLY B 235 " occ=0.68 ... (6 atoms not shown) pdb=" O BGLY B 235 " occ=0.32 residue: pdb=" N ASER C 234 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER C 234 " occ=0.51 residue: pdb=" N AGLY C 235 " occ=0.49 ... (6 atoms not shown) pdb=" O BGLY C 235 " occ=0.51 Time building chain proxies: 14.27, per 1000 atoms: 1.01 Number of scatterers: 14196 At special positions: 0 Unit cell: (90.882, 86.394, 184.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2794 8.00 N 2420 7.00 C 8916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 4.6 seconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 39 sheets defined 7.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.774A pdb=" N ASN A 157 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 159 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.502A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'B' and resid 110 through 123 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 153 through 160 removed outlier: 4.498A pdb=" N ALA B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.692A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.841A pdb=" N ILE C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.754A pdb=" N LYS C 158 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.810A pdb=" N GLY C 167 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 4.082A pdb=" N VAL A 8 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 81 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 49 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.604A pdb=" N GLN A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 75 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 66 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.634A pdb=" N VAL A 49 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 81 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 8 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 198 removed outlier: 5.779A pdb=" N TYR A 253 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 252 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP A 288 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 254 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 307 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 392 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 370 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET A 394 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 415 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 417 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 416 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER A 451 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE A 418 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 448 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N SER A 481 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 450 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 502 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 521 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.011A pdb=" N LEU A 230 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU A 296 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 321 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 349 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 319 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 321 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLN A 353 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 323 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 470 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.552A pdb=" N ILE A 378 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N CYS A 377 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.529A pdb=" N GLN A 355 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 357 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 362 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 421 through 423 removed outlier: 6.128A pdb=" N SER A 421 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AB4, first strand: chain 'A' and resid 555 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.555A pdb=" N VAL B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 34 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 101 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.168A pdb=" N VAL B 49 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 198 removed outlier: 5.716A pdb=" N LEU B 196 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.540A pdb=" N THR B 260 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 213 through 214 removed outlier: 5.759A pdb=" N LEU B 213 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY B 267 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 241 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 298 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.687A pdb=" N ALA B 383 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE B 352 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.801A pdb=" N ALA B 368 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.023A pdb=" N CYS B 335 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 378 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 337 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP B 422 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 423 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 483 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS B 506 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 390 through 392 removed outlier: 3.860A pdb=" N ASP B 391 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 415 " --> pdb=" O ASP B 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AC7, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC8, first strand: chain 'C' and resid 30 through 31 removed outlier: 4.611A pdb=" N VAL C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD1, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.739A pdb=" N THR C 260 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 213 through 215 removed outlier: 7.329A pdb=" N ASN C 266 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 300 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 268 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 296 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 321 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 323 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C 349 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA C 383 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL C 408 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 384 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.479A pdb=" N LEU C 254 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 283 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LYS C 308 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP C 285 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 310 " --> pdb=" O TRP C 285 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE C 287 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 330 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS C 308 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 332 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 310 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.825A pdb=" N CYS C 312 " --> pdb=" O HIS C 336 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER C 338 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 314 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS C 335 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 378 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 337 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 355 through 356 removed outlier: 3.903A pdb=" N GLN C 355 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.304A pdb=" N CYS C 389 " --> pdb=" O ASN C 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 416 through 418 removed outlier: 6.514A pdb=" N PHE C 416 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C 448 " --> pdb=" O PHE C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 495 through 497 removed outlier: 6.436A pdb=" N ARG C 516 " --> pdb=" O VAL C 495 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 497 " --> pdb=" O ARG C 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 512 through 514 removed outlier: 5.842A pdb=" N LEU C 512 " --> pdb=" O THR C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.641A pdb=" N VAL C 522 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 568 through 570 Processing sheet with id=AE3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.210A pdb=" N MET C 617 " --> pdb=" O LEU C 584 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4768 1.34 - 1.46: 3270 1.46 - 1.58: 6346 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 14477 Sorted by residual: bond pdb=" CA THR B 430 " pdb=" CB THR B 430 " ideal model delta sigma weight residual 1.528 1.562 -0.034 2.61e-02 1.47e+03 1.69e+00 bond pdb=" C VAL C 549 " pdb=" N PRO C 550 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" CG MET A 291 " pdb=" SD MET A 291 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" N GLU A 532 " pdb=" CA GLU A 532 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CB VAL B 74 " pdb=" CG2 VAL B 74 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 ... (remaining 14472 not shown) Histogram of bond angle deviations from ideal: 95.59 - 103.28: 118 103.28 - 110.97: 5360 110.97 - 118.66: 6105 118.66 - 126.35: 7970 126.35 - 134.05: 161 Bond angle restraints: 19714 Sorted by residual: angle pdb=" CA GLY C 554 " pdb=" C GLY C 554 " pdb=" N ILE C 555 " ideal model delta sigma weight residual 114.58 117.93 -3.35 8.60e-01 1.35e+00 1.51e+01 angle pdb=" CA MET A 394 " pdb=" CB MET A 394 " pdb=" CG MET A 394 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET A 617 " pdb=" CG MET A 617 " pdb=" SD MET A 617 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " ideal model delta sigma weight residual 113.65 109.15 4.50 1.47e+00 4.63e-01 9.38e+00 angle pdb=" CA MET A 617 " pdb=" CB MET A 617 " pdb=" CG MET A 617 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.08e+00 ... (remaining 19709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7806 17.83 - 35.65: 624 35.65 - 53.48: 114 53.48 - 71.30: 40 71.30 - 89.13: 17 Dihedral angle restraints: 8601 sinusoidal: 3234 harmonic: 5367 Sorted by residual: dihedral pdb=" CA VAL A 282 " pdb=" C VAL A 282 " pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP C 372 " pdb=" C ASP C 372 " pdb=" N SER C 373 " pdb=" CA SER C 373 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU C 321 " pdb=" C LEU C 321 " pdb=" N HIS C 322 " pdb=" CA HIS C 322 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1496 0.039 - 0.079: 466 0.079 - 0.118: 253 0.118 - 0.157: 38 0.157 - 0.197: 3 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CG LEU C 512 " pdb=" CB LEU C 512 " pdb=" CD1 LEU C 512 " pdb=" CD2 LEU C 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE C 476 " pdb=" CA ILE C 476 " pdb=" CG1 ILE C 476 " pdb=" CG2 ILE C 476 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR A 249 " pdb=" CA THR A 249 " pdb=" OG1 THR A 249 " pdb=" CG2 THR A 249 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 2253 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 440 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO C 441 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 115 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO C 116 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 145 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 146 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.033 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 919 2.73 - 3.27: 15089 3.27 - 3.81: 23416 3.81 - 4.36: 28027 4.36 - 4.90: 48418 Nonbonded interactions: 115869 Sorted by model distance: nonbonded pdb=" NH2 ARG C 339 " pdb=" O SER C 343 " model vdw 2.183 2.520 nonbonded pdb=" NH1 ARG B 365 " pdb=" OD1 ASP B 388 " model vdw 2.242 2.520 nonbonded pdb=" OG ASER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.244 2.440 nonbonded pdb=" OG BSER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.251 2.440 nonbonded pdb=" O PRO A 550 " pdb=" ND2 ASN A 573 " model vdw 2.269 2.520 ... (remaining 115864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'B' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'C' and (resid 5 through 157 or resid 159 through 233 or resid 236 throug \ h 337 or resid 339 through 344 or resid 346 through 418 or resid 420 through 430 \ or resid 432 through 438 or resid 440 through 459 or resid 461 through 508 or r \ esid 510 through 520 or resid 522 through 555 or resid 557 through 581 or resid \ 583 through 590 or resid 592 through 603 or resid 605 through 620 or resid 622 t \ hrough 623)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8916 2.51 5 N 2420 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.830 Check model and map are aligned: 0.200 Process input model: 50.600 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14477 Z= 0.223 Angle : 0.609 9.245 19714 Z= 0.326 Chirality : 0.048 0.197 2256 Planarity : 0.005 0.067 2592 Dihedral : 14.529 89.126 5179 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.19), residues: 1867 helix: 0.35 (0.58), residues: 91 sheet: -2.00 (0.26), residues: 447 loop : -2.09 (0.16), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.655 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2102 time to fit residues: 18.1525 Evaluate side-chains 39 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 88 optimal weight: 50.0000 chunk 107 optimal weight: 40.0000 chunk 168 optimal weight: 20.0000 overall best weight: 8.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14477 Z= 0.292 Angle : 0.596 6.919 19714 Z= 0.320 Chirality : 0.048 0.221 2256 Planarity : 0.005 0.065 2592 Dihedral : 5.010 45.341 2014 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1867 helix: 0.47 (0.59), residues: 90 sheet: -2.08 (0.25), residues: 462 loop : -2.10 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.705 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.2059 time to fit residues: 16.8983 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1268 time to fit residues: 2.7355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 30.0000 chunk 52 optimal weight: 0.0040 chunk 139 optimal weight: 30.0000 chunk 114 optimal weight: 40.0000 chunk 46 optimal weight: 50.0000 chunk 168 optimal weight: 30.0000 chunk 181 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 135 optimal weight: 10.0000 overall best weight: 10.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 14477 Z= 0.322 Angle : 0.600 7.090 19714 Z= 0.322 Chirality : 0.048 0.184 2256 Planarity : 0.005 0.065 2592 Dihedral : 5.121 46.666 2014 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.19), residues: 1867 helix: 0.32 (0.58), residues: 91 sheet: -2.17 (0.25), residues: 462 loop : -2.17 (0.16), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.836 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.2198 time to fit residues: 17.3641 Evaluate side-chains 41 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1490 time to fit residues: 2.4857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 50.0000 chunk 88 optimal weight: 30.0000 chunk 160 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14477 Z= 0.239 Angle : 0.576 16.084 19714 Z= 0.303 Chirality : 0.047 0.169 2256 Planarity : 0.004 0.064 2592 Dihedral : 4.962 46.757 2014 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.19), residues: 1867 helix: 0.46 (0.58), residues: 91 sheet: -2.11 (0.25), residues: 462 loop : -2.12 (0.16), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 1.768 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.2288 time to fit residues: 19.0520 Evaluate side-chains 41 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 40.0000 chunk 160 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14477 Z= 0.133 Angle : 0.527 12.285 19714 Z= 0.276 Chirality : 0.047 0.205 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.562 43.511 2014 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.19), residues: 1867 helix: 0.74 (0.56), residues: 97 sheet: -1.90 (0.26), residues: 441 loop : -2.08 (0.16), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 1.974 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.2377 time to fit residues: 22.0953 Evaluate side-chains 43 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1380 time to fit residues: 2.8921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 0.0670 chunk 59 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 overall best weight: 9.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 14477 Z= 0.304 Angle : 0.599 10.970 19714 Z= 0.319 Chirality : 0.048 0.185 2256 Planarity : 0.005 0.063 2592 Dihedral : 4.926 45.446 2014 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1867 helix: 0.71 (0.58), residues: 90 sheet: -2.11 (0.25), residues: 453 loop : -2.09 (0.16), residues: 1324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 1.775 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.2185 time to fit residues: 19.0973 Evaluate side-chains 46 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1380 time to fit residues: 3.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 178 optimal weight: 50.0000 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14477 Z= 0.254 Angle : 0.578 9.716 19714 Z= 0.306 Chirality : 0.047 0.183 2256 Planarity : 0.004 0.064 2592 Dihedral : 4.895 46.518 2014 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1867 helix: 0.70 (0.58), residues: 91 sheet: -2.13 (0.25), residues: 461 loop : -2.12 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 1.787 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.2217 time to fit residues: 17.5246 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1272 time to fit residues: 2.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 53 optimal weight: 0.0570 chunk 35 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 113 optimal weight: 0.0570 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 overall best weight: 7.6224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 14477 Z= 0.256 Angle : 0.575 9.012 19714 Z= 0.306 Chirality : 0.047 0.174 2256 Planarity : 0.004 0.064 2592 Dihedral : 4.898 47.134 2014 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1867 helix: 0.70 (0.58), residues: 91 sheet: -2.16 (0.25), residues: 453 loop : -2.09 (0.16), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2223 time to fit residues: 17.5520 Evaluate side-chains 43 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 40.0000 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 14477 Z= 0.230 Angle : 0.566 8.565 19714 Z= 0.300 Chirality : 0.047 0.172 2256 Planarity : 0.004 0.064 2592 Dihedral : 4.861 46.892 2014 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.19), residues: 1867 helix: 0.73 (0.58), residues: 91 sheet: -2.11 (0.26), residues: 449 loop : -2.11 (0.16), residues: 1327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2239 time to fit residues: 17.6042 Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 40.0000 chunk 107 optimal weight: 40.0000 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 116 optimal weight: 50.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 14477 Z= 0.165 Angle : 0.544 9.709 19714 Z= 0.286 Chirality : 0.047 0.159 2256 Planarity : 0.004 0.063 2592 Dihedral : 4.651 44.872 2014 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.19), residues: 1867 helix: 0.78 (0.56), residues: 97 sheet: -2.00 (0.26), residues: 431 loop : -2.07 (0.16), residues: 1339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.883 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2197 time to fit residues: 17.0375 Evaluate side-chains 41 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 40.0000 chunk 44 optimal weight: 30.0000 chunk 135 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.082096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056432 restraints weight = 270899.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059446 restraints weight = 58640.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061392 restraints weight = 27853.404| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 14477 Z= 0.140 Angle : 0.532 8.765 19714 Z= 0.280 Chirality : 0.047 0.156 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.425 41.767 2014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.19), residues: 1867 helix: 0.87 (0.57), residues: 97 sheet: -1.89 (0.26), residues: 448 loop : -2.04 (0.16), residues: 1322 =============================================================================== Job complete usr+sys time: 2473.60 seconds wall clock time: 47 minutes 3.19 seconds (2823.19 seconds total)